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Tresslers Group Intelligence Matrix

batch_optimize_codon

Batch codon optimization for teams and agents: optimize up to 50 protein or cDNA coding sequences in one call with the Logos bio-engine (CAI maximization, GC harmonization, restriction-site avoidance, consensus leaders). Free tier: 100 sequences per caller per day. Overage is $0.50 USDC per 10 sequences ($0.05/sequence) on Base, verified on-chain — pass payment_proof when the batch exceeds the free tier. Research Use Only (RUO); select-agent sequences prohibited.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
hostNoTarget expression organism: 'e_coli', 'h_sapiens' (HEK293), 'c_griseus' (CHO), 's_cerevisiae', 'p_pastoris', 'v_natriegens', 'n_benthamiana', 'a_thaliana'. Default: 'e_coli'
api_keyNoOptional stable caller identifier for quota tracking (useful behind shared IPs). Self-asserted in v1.
gc_targetNoTarget global GC percentage (e.g., 52 for E. coli, 58 for Human). Optional.
sequencesYesAmino acid sequences (single-letter uppercase) or DNA coding sequences to optimize. Max 50 per call; max 5000 characters each.
payment_proofNoUSDC transaction hash on Base. Required when the batch exceeds the 100/day free tier.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
contentNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. Added

TDQS

A4/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With annotations empty, the description carries the full burden and does substantial work: it discloses a per-caller quota (100 sequences/day), overage pricing ($0.05/sequence on Base), on-chain verification, and the payment_proof requirement trigger, plus a legal/usage restriction. It still leaves the success/failure behavior and quota-exhaustion handling unstated, so it is strong but not exhaustive.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Front-loaded with the core capability, then limits, then payment terms, then restrictions — a logical order with no filler sentences. It is dense with parentheticals and monetary detail packed into long clauses, which slightly taxes readability but every clause earns its place.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a batch mutation/compute tool with an output schema present, the description supplies everything an agent needs: batch ceiling, per-sequence limit context, quota, pricing and payment trigger, and compliance restrictions. Return values are covered by the output schema, so nothing material is missing.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, and the schema itself already documents host, api_key, gc_target, sequences limits, and the payment_proof condition. The description restates the free-tier threshold that gates payment_proof but adds no new semantics (formats, ranges, defaults) beyond the schema, so baseline 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource (codon optimization of up to 50 protein or cDNA sequences per call) and enumerates the engine's objectives (CAI maximization, GC harmonization, restriction-site avoidance). The 'Batch ... in one call' framing implicitly distinguishes it from the optimize_codon sibling, but it never names that alternative, so differentiation is inferred rather than explicit.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Gives concrete use context: batch workflows for teams/agents, the 100-sequence/day free tier, and the condition that triggers payment_proof (batch exceeding the free tier). It also states a prohibitive condition (RUO, no select-agent sequences). What it lacks is an explicit routing rule to the single-sequence optimize_codon sibling.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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